Closed houruiyan closed 9 months ago
Hi Dr chung,
I have another question.
I want to run proactiv from bam file. The bam file in the red frame was used.
This is my script
library(proActiv) #BiocManager::install("BSgenome.Mmusculus.UCSC.mm10") mouse.gtf.file <- '/mnt/ruiyanhou/nfs_share2/RNA_seq_organ_species/ref_annotation/Mus_musculus.GRCm38.77.gtf.gz' mouse_annotation <- preparePromoterAnnotation(file = mouse.gtf.file, species = 'Mus_musculus') mouse_bam_file<-'/mnt/ruiyanhou/nfs_share2/RNA_seq_organ_species/bam_file/mouse/5360sTS.Mouse.Kidney.9wpb.Male.sorted.bam' mouse_result <- proActiv(files = mouse_bam_file, promoterAnnotation = mouse_annotation,genome='mm10',ncores=1) ## Removes single-exon transcripts / promoters by eliminating promoter counts that are NA result <- result[complete.cases(assays(result)$promoterCounts),] ## export result result_df <- rowData(result) result_df$txId <- vapply(result_df$txId, paste, collapse = ", ", character(1L)) write.table(result_df, "/mnt/ruiyanhou/nfs_share2/RNA_seq_organ_species/proactiv_result/mouse/5360sTS.Mouse.Kidney.9wpb.Male.rowData.tsv", sep = "\t", quote = F) result_absolutePromoterActivity_df <- assays(result)$absolutePromoterActivity write.table(result_absolutePromoterActivity_df, "/mnt/ruiyanhou/nfs_share2/RNA_seq_organ_species/proactiv_result/mouse/5360sTS.Mouse.Kidney.9wpb.Male.activ.tsv", sep = "\t", quote = F)
Then I run [ruiyanhou@CPU3:RNA_seq_organ_species]$ nohup Rscript run_proactiv.R &
[ruiyanhou@CPU3:RNA_seq_organ_species]$ nohup Rscript run_proactiv.R &
But I always get this error
In addition, when I run in the Rstudio, it also aborted suddendly.
Could you help me? Thank you very much!
This solved. Thanks! When I changed to another server. this error will not appear.
Hi Dr chung,
I have another question.
I want to run proactiv from bam file. The bam file in the red frame was used.
This is my script
Then I run
[ruiyanhou@CPU3:RNA_seq_organ_species]$ nohup Rscript run_proactiv.R &
But I always get this error
In addition, when I run in the Rstudio, it also aborted suddendly.
Could you help me? Thank you very much!